pymafft

Python bindings for MAFFT-rs, a Rust reimplementation of the MAFFT multiple sequence alignment tool.

Installation

pip install pymafft

Quick start

import pymafft

# Align protein sequences
result = pymafft.align([
    "ACDEFGHIKLMNPQRSTVWY",
    "ACDEFHIKLMNPQRSTVWY",
    "ACDEHIKLMNPQRSTVWY",
])

for seq in result:
    print(f"{seq.name}: {seq.sequence}")

print(f"Alignment width: {result.width}")

Usage

Align from a list of sequences

# Auto-named (seq_1, seq_2, ...)
result = pymafft.align(["ACDEFGHIK", "ACDEFHIK", "ACDHIK"])

# Named sequences
result = pymafft.align([
    ("human", "ACDEFGHIKLMNP"),
    ("mouse", "ACDEFHIKLMNP"),
    ("fish",  "ACDEHIKLMNP"),
])

Align from a FASTA file

result = pymafft.align_file("sequences.fasta")

Align from a FASTA string

fasta = ">s1\nACDEFGHIK\n>s2\nACDEFHIK\n"
result = pymafft.align_fasta_string(fasta)

Choose an alignment strategy

# FFT-NS-2: fast default
result = pymafft.align(seqs, strategy="fftns2")

# G-INS-i: global iterative (accurate, for globally alignable sequences)
result = pymafft.align(seqs, strategy="ginsi")

# L-INS-i: local iterative (most accurate for <200 sequences)
result = pymafft.align(seqs, strategy="linsi")

# E-INS-i: generalized affine (for sequences with large internal gaps)
result = pymafft.align(seqs, strategy="einsi")

# FFT-NS-i: progressive + iterative refinement
result = pymafft.align(seqs, strategy="fftnsi", maxiterate=100)

# --auto: let MAFFT pick from the number and length of the sequences
result = pymafft.align(seqs, strategy="auto")

CLI-equivalent options

Every keyword is one mafft-rs command-line flag, applied by the CLI's own flag layer, so the result is byte-identical to the command line's for the same flags.

# `mafft --auto --adjustdirection --thread 1 --nuc` over in-memory records
result = pymafft.align(genes, strategy="auto", adjust_direction=True,
                       threads=1, seq_type="nuc")

# Substitution matrix and gap penalties (`--bl 50 --op 1.0 --ep 0.2`)
result = pymafft.align(seqs, scoring="bl50", gap_open=1.0, gap_extend=0.2)

# Guide-tree order output, one more tree rebuild
result = pymafft.align(seqs, reorder=True, retree=3)

# Progress lines (the CLI's stderr) to a callable; quiet by default
result = pymafft.align(seqs, strategy="auto", progress=print)

# Any other flag, verbatim
result = pymafft.run(["--nofft", "--maxiterate", "2", "--quiet"], seqs)

Failures raise pymafft.MafftError (a ValueError) with the CLI's exit code in .code and stderr text in .message, e.g. Illegal character U for a residue outside the alphabet. Nucleotide output is lowercase and protein output uppercase, as with C MAFFT.

Work with results

result = pymafft.align(["ACDEFGHIK", "ACDEFHIK"])

# Access sequences
result.nseq              # number of sequences
result.width             # alignment width (columns)
result[0].name           # sequence name
result[0].sequence       # aligned sequence (with gaps)
result[0].ungapped()     # sequence without gaps

# Export
result.to_fasta()        # FASTA-formatted string
result.to_tuples()       # list of (name, sequence) tuples
result.to_biopython()    # Bio.Align.MultipleSeqAlignment (Biopython imported lazily)

# Iterate
for seq in result:
    print(seq.name, len(seq))

Supported strategies

Strategy Flag Description
fftns2 default Fast progressive alignment
fftnsi --maxiterate N Progressive + iterative refinement
ginsi --globalpair Global iterative (accurate)
linsi --localpair Local iterative (most accurate for <200 seqs)
einsi --genafpair Generalized affine (large internal gaps)
auto --auto Chosen from sequence count and length

License

  • Rust code: MIT
  • Original MAFFT algorithm: BSD-3-Clause

Based on MAFFT by Kazutaka Katoh.

Project links

Data verified by PyPI on Sep 6, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for luksgrin from gravatar.com luksgrin

Credits

Author: Lucas Goiriz

GitHub Statistics

Data verified by PyPI on Sep 6, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT AND BSD-3-Clause)

Requires

Python >=3.9

Provides Extra

test

Tags

bioinformatics alignment msa fasta mafft sequence

Classifiers

Report project as malware

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This release

0.2.0 This release

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0.1.0

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Yanked reason: Partial release; superseded by 0.1.1

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